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(-) Description

Title :  CRYSTAL STRUCTURE OF MUTANT ENZYME Y32F/D103L OF KETOSTEROID ISOMERASE FROM PSEUDOMONAS PUTIDA BIOTYPE B
 
Authors :  D. S. Jang, H. J. Cha, K. Y. Choi
Date :  30 May 04  (Deposition) - 08 Jul 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Isomerase, Coneshell, Closed Barrel, Curved B-Sheet (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. S. Jang, H. J. Cha, S. S. Cha, B. H. Hong, N. C. Ha, J. Y. Lee, B. H. Oh, H. S. Lee, K. Y. Choi
Structural Double-Mutant Cycle Analysis Of A Hydrogen Bond Network In Ketosteroid Isomerase From Pseudomonas Putida Biotype B.
Biochem. J. V. 382 967 2004
PubMed-ID: 15228388  |  Reference-DOI: 10.1042/BJ20031871
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - STEROID DELTA-ISOMERASE
    Chains: A, B
    EC Number: 5.3.3.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKK223-3
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: PSEUDOMONAS PUTIDA
    Organism Taxid: 303
    Synonym: DELTA-5-3-KETOSTEROID ISOMERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1VZZ)

(-) Sites  (0, 0)

(no "Site" information available for 1VZZ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VZZ)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asp A:40 -Pro A:41
2Asp B:40 -Pro B:41

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VZZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VZZ)

(-) Exons   (0, 0)

(no "Exon" information available for 1VZZ)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:120
 aligned with SDIS_PSEPU | P07445 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:126
                                    11        21        31        41        51        61        71        81        91       101       111       121      
           SDIS_PSEPU     2 NLPTAQEVQGLMARYIELVDVGDIEAIVQMYADDATVEDPFGQPPIHGREQIAAFYRQGLGGGKVRACLTGPVRASHNGCGAMPFRVEMVWNGQPCALDVIDVMRFDEHGRIQTMQAYWSEVNLSV 127
               SCOP domains d1vzza_ A: Delta-5-3-ketosteroid isomerase, steroid delta-iso  merase, KSI                                                     SCOP domains
               CATH domains 1vzzA00 A:2-127  [code=3.10.450.50, no name defined]                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeee.......eehhhhhhhhhhhhhh--................eeeeeeeeee.----.eeeeeeeeeee.....eeeeeee.hhh.ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vzz A   2 NLPTAQEVQGLMARYIELVDVGDIEAIVQMFADDATVEDPFGQPPIHGREQIAAFYRQGLG--KVRACLTGPVRASHNGCGAMPFRVEMV----PCALDVILVMRFDEHGRIQTMQAYWSEVNLSV 127
                                    11        21        31        41        51        61|  |    71        81        91    |  101       111       121      
                                                                                       62 65                        91   96                               


Chain B from PDB  Type:PROTEIN  Length:124
 aligned with SDIS_PSEPU | P07445 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:126
                                    11        21        31        41        51        61        71        81        91       101       111       121      
           SDIS_PSEPU     2 NLPTAQEVQGLMARYIELVDVGDIEAIVQMYADDATVEDPFGQPPIHGREQIAAFYRQGLGGGKVRACLTGPVRASHNGCGAMPFRVEMVWNGQPCALDVIDVMRFDEHGRIQTMQAYWSEVNLSV 127
               SCOP domains d1vzzb_ B: Delta-5-3-ketosteroid isomerase, steroid delta-iso  merase, KSI                                                     SCOP domains
               CATH domains 1vzzB00 B:2-127  [code=3.10.450.50, no name defined]                                                                           CATH domains
           Pfam domains (1) ------NTF2-1vzzB01 B:8-127                                                                                                     Pfam domains (1)
           Pfam domains (2) ------NTF2-1vzzB02 B:8-127                                                                                                     Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeee.......eehhhhhhhhhhhhhh--................eeeeeeeeeeee..eeeeeeeeeeeee.....eeeeeee.hhh.ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vzz B   2 NLPTAQEVQGLMARYIELVDVGDIEAIVQMFADDATVEDPFGQPPIHGREQIAAFYRQGLG--KVRACLTGPVRASHNGCGAMPFRVEMVWNGQPCALDVILVMRFDEHGRIQTMQAYWSEVNLSV 127
                                    11        21        31        41        51        61|  |    71        81        91       101       111       121      
                                                                                       62 65
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: NTF2 (66)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SDIS_PSEPU | P07445)
molecular function
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0004769    steroid delta-isomerase activity    Catalysis of the reaction: a 3-oxo-delta(5)-steroid = a 3-oxo-delta(4)-steroid.
biological process
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0008202    steroid metabolic process    The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.

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  Cis Peptide Bonds
    Asp A:40 - Pro A:41   [ RasMol ]  
    Asp B:40 - Pro B:41   [ RasMol ]  
 

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  5.3.3.1
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        SDIS_PSEPU | P07445: 1c7h 1cqs 1dmm 1dmn 1dmq 1e3r 1e3v 1e97 1ea2 1gs3 1k41 1ogx 1oh0 1oho 1opy 1w00 1w01 1w02 1w6y 2inx 2pzv 3cpo 3fzw 3ipt 3ows 3owu 3owy 3ox9 3oxa 3rgr 3sed 3t8n 3vgn 3vsy 4cdl 4k1u 4k1v 5ai1 5d81 5d82 5d83 5g2g 5kp1 5kp3 5kp4

(-) Related Entries Specified in the PDB File

1c7h CRYSTAL STRUCTURE OF A MUTANT R75A IN KETOSTEROID ISOMERASE FROM PSEDOMONAS PUTIDA BIOTYPE B
1cqs CRYSTAL STRUCTURE OF D103E MUTANT WITH EQUILENINEOF KSI INPSEUDOMONAS PUTIDA
1dmm CRYSTAL STRUCTURES OF MUTANT ENZYMES Y57F OF KETOSTEROID ISOMERASE FROM PSEUDOMONAS PUTIDA BIOTYPE B
1dmn CRYSTAL STRUCTURE OF MUTANT ENZYME Y32F/Y57F OF KETOSTEROID ISOMERASE FROM PSEUDOMONAS PUTIDA BIOTYPE B
1dmq CRYSTAL STRUCTURE OF MUTANT ENZYME Y32F OF KETOSTEROID ISOMERASE FROM PSEUDOMONAS PUTIDA BIOTYPE B
1e3r CRYSTAL STRUCTURE OF KETOSTEROID ISOMERASE MUTANT D40N (D38N TI NUMBERING) FROM PSEUDOMONAS PUTIDA COMPLEXED WITH ANDROSTEN- 3BETA-OL-17-ONE
1e3v CRYSTAL STRUCTURE OF KETOSTEROID ISOMERASE FROM PSEDOMONAS PUTIDA COMPLEXED WITH DEOXYCHOLATE
1e97 CRYSTAL STRUCTURE OF KETOSTEROID ISOMERASE FROM PSEUDOMONAS PUTIDA ; TRIPLE MUTANT Y16F/ Y32F/Y57F
1ea2 PSEUDOREVERSION OF THE CATALYTIC ACTIVITY OF Y14F BY THE ADDITIONAL TYROSIN- TO - PHENYLALANINE SUBSTITUTION(S) IN THE HYDROGEN BOND NETWORK OF %D5-3-KETOSTEROID ISOMERASE FROM PHEUDOMONAS PUTIDA BIOTYPE B
1gs3 HIGH RESOLUTION CRYSTAL STRUCTURE OF PI DELTA-5-3-KETOSTEROID ISOMERASE MUTANTS Y30F /Y55F/Y115F/D38N (Y32F/Y57F/Y119F/D40N, PI NUMBERING)COMPLEXED WITH EQUILENIN AT 2. 1 A RESOLUTION
1k41 CRYSTAL STRUCTURE OF KSI Y57S MUTANT
1ogx HIGH RESOLUTION CRYSTAL STRUCTURE OF KETOSTEROID ISOMERASE MUTANT D40N(D38N, TI NUMBERING) COMPLEXED WITH EQUILENIN AT 2.0 A RESOLUTION.
1oh0 CRYSTAL STRUCTURE OF KETOSTEROID ISOMERASE COMPLEXED WITH EQUILENIN
1oho CRYSTAL STRUCTURE OF KETOSTEROID ISOMERASE Y16F/D40N MUTANT COMPLEXED WITH EQUILENIN
1opy KSI
1w00 CRYSTAL STRUCTURE OF KETOSTEROID ISOMERASE MUTANT ENZYMES D103L
1w01 CRYSTAL STRUCTURE OF KETOSTEROID ISOMERASE MUTANT ENZYMES Y57F/D103L
1w02 CRYSTAL STRUCTURE OF KETOSTEROID ISOMERASE MUTANT ENZYMES Y16F/D103L